The International Maritime Organization forecasts that greenhouse gasses produced by ships will increase rapidly in the near future, unless precautions are taken now. This will require all ships to reduce their emissions, especially container vessels which are producing the most emissions. One way of reducing emissions, with existing technology, is to switch to alternative fuels. Making this switch is risky as there are many economic and regulatory uncertainties, which the ship has to survive over its lifetime. This makes it difficult to see which alternative fuel is a better option or not. There is no existing study which makes a comparison between alternative fuels which also takes future uncertainty into account. The aim of this study is to develop an approach to assess alternative fuel types for robust ultra large container vessels, while taking economic and regulatory uncertainty into account. For this purpose, Robust Decision Making was chosen as the most suitable method. A method which has been used in different areas, but will be implemented for the first time for a subject relating to ship design. Implementing this method required the development of a parametric design tool for ultra large container vessels. Results show that liquefied natural gas is the most robust option amongst the considered alternative fuels. It would have a good economic performance, while reducing emissions. Non-carbon fuels, such as hydrogen and ammonia, would practically eliminate emissions but do not perform well financially.